Genome analyses of the microalga Picochlorum provide insights into the evolution of thermotolerance in the green lineage

While the molecular events involved in cell responses to heat stress have been extensively studied, our understanding of the genetic basis of basal thermotolerance, and particularly its evolution within the green lineage, remains limited. Here, we present the 13.3-Mb haploid genome and transcriptomes of a halotolerant and thermotolerant unicellular green alga, Picochlorum costavermella (Trebouxiophyceae) to investigate the evolution of the genomic basis of thermotolerance. Differential gene expression at high and standard temperatures revealed that more of the gene families containing up-regulated genes at high temperature were recently evolved, and less originated at the ancestor of green plants. Inversely, there was an excess of ancient gene families containing transcriptionally repressed genes. Interestingly, there is a striking overlap between the thermotolerance and halotolerance transcriptional rewiring, as more than one-third of the gene families up-regulated at 35 degrees C were also up-regulated under variable salt concentrations in Picochlorum SE3. Moreover, phylogenetic analysis of the 9,304 protein coding genes revealed 26 genes of horizontally transferred origin in P. costavermella, of which five were differentially expressed at higher temperature. Altogether, these results provide new insights about how the genomic basis of adaptation to halo- and thermotolerance evolved in the green lineage

Spontaneous mutation rate in the smallest photosynthetic eukaryotes

Mutation is the ultimate source of genetic variation, and knowledge of mutation rates is fundamental for our understanding of all evolutionary processes. High throughput sequencing of mutation accumulation lines has provided genome wide spontaneous mutation rates in a dozen model species, but estimates from nonmodel organisms from much of the diversity of life are very limited. Here, we report mutation rates in four haploid marine bacterial-sized photosynthetic eukaryotic algae; Bathycoccus prasinos, Ostreococcus tauri, Ostreococcus mediterraneus, and Micromonas pusilla. The spontaneous mutation rate between species varies from μ = 4.4 × 10−10 to 9.8 × 10−10 mutations per nucleotide per generation. Within genomes, there is a two-fold increase of the mutation rate in intergenic regions, consistent with an optimization of mismatch and transcription-coupled DNA repair in coding sequences. Additionally, we show that deviation from the equilibrium GC content increases the mutation rate by ∼2% to ∼12% because of a GC bias in coding sequences. More generally, the difference between the observed and equilibrium GC content of genomes explains some of the inter-specific variation in mutation rates

Population genomics of picophytoplankton unveils novel chromosome hypervariability

Tiny photosynthetic microorganisms that form the picoplankton (between 0.3 and 3 mm in diameter) are at the base of the food web in many marine ecosystems, and their adaptability to environmental change hinges on standing genetic variation. Although the genomic and phenotypic diversity of the bacterial component of the oceans has been intensively studied, little is known about the genomic and phenotypic diversity within each of the diverse eukaryotic species present. We report the level of genomic diversity in a natural population of Ostreococcus tauri (Chlorophyta, Mamiellophyceae), the smallest photosynthetic eukaryote. Contrary to the expec- tations of clonal evolution or cryptic species, the spectrum of genomic polymorphism observed suggests a large panmictic population (an effective population size of 1.2 × 107) with pervasive evidence of sexual reproduction. De novo assemblies of low-coverage chromosomes reveal two large candidate mating-type loci with suppressed recom- bination, whose origin may pre-date the speciation events in the class Mamiellophyceae. This high genetic diversity is associated with large phenotypic differences between strains. Strikingly, resistance of isolates to large double- stranded DNA viruses, which abound in their natural environment, is positively correlated with the size of a single hypervariable chromosome, which contains 44 to 156 kb of strain-specific sequences. Our findings highlight the role of viruses in shaping genome diversity in marine picoeukaryotes

Estimation of mutation rates : implications for diversification and evolution of eukaryotic phytoplankton

Les mutations sont la principale source de diversité sur laquelle agit la sélection pour permettre aux espèces de s'adapter. Les études de l'effet des mutations sur la survie et du taux de mutation sont donc essentielles pour mieux comprendre l'évolution. Par une approche d'expérience d'accumulation de mutations, nous étudions ces deux questions chez cinq modèles d'algues vertes (Ostreococcus tauri, O. mediterraneus, Bathycoccus prasinos, Micromonas pusilla, et Picochlorum RCC4223). Il est mis en évidence une diminution de la fitness au cours du temps en raison des mutations délétères, et une importante interaction génotype-environnement sur l'effet des mutations. Le taux de mutation varie aux échelles intra-génomique et inter-spécifique, avec deux principaux résultats: une augmentation du taux de mutation dans les régions non codantes et une augmentation du taux de mutation avec la taille du génome chez les eucaryotes et en fonction de l'écart à l'équilibre en GC du génome. Aussi, l'assemblage et l'annotation d'une picoalgue du genre Picochlorum permettent d'étudier le rôle des transferts horizontaux de gènes chez les Chlorophytes.Mutations are the main source of diversity on which selection acts to allow species to adapt. Studies of the effect of mutations on survival and estimation of spontaneous mutation rates are essential to better understand evolution. Using mutation accumulation experimental approach, we investigated the issues of mutation effects and mutation rate in five models of green algae (Ostreococcus tauri, O. mediterraneus, Bathycoccus Prasinos, Micromonas pusilla, and Picochlorum RCC4223). It highlighted a decline in fitness over time because of deleterious mutations, and a significant genotype-environment interaction on the fitness effect of mutations. The mutation rate varies at inter-specific and intra-genomic scales, with two main results: a raise of the mutation rate in non-coding regions in accordance with trancriptional-coupled repair, and an increase of the mutation rate with an increase of the genome size in eukaryotes and the GC content deviation from the equilibrium. Also, a new Picochlorum genome is provided to investigate the role of horizontal gene transfer in the Chlorophyta group

Estimation des taux de mutation : implications pour la diversification et l'évolution du phytoplancton eucaryote

Mutations are the main source of diversity on which selection acts to allow species to adapt. Studies of the effect of mutations on survival and estimation of spontaneous mutation rates are essential to better understand evolution. Using mutation accumulation experimental approach, we investigated the issues of mutation effects and mutation rate in five models of green algae (Ostreococcus tauri, O. mediterraneus, Bathycoccus Prasinos, Micromonas pusilla, and Picochlorum RCC4223). It highlighted a decline in fitness over time because of deleterious mutations, and a significant genotype-environment interaction on the fitness effect of mutations. The mutation rate varies at inter-specific and intra-genomic scales, with two main results: a raise of the mutation rate in non-coding regions in accordance with trancriptional-coupled repair, and an increase of the mutation rate with an increase of the genome size in eukaryotes and the GC content deviation from the equilibrium. Also, a new Picochlorum genome is provided to investigate the role of horizontal gene transfer in the Chlorophyta group.Les mutations sont la principale source de diversité sur laquelle agit la sélection pour permettre aux espèces de s'adapter. Les études de l'effet des mutations sur la survie et du taux de mutation sont donc essentielles pour mieux comprendre l'évolution. Par une approche d'expérience d'accumulation de mutations, nous étudions ces deux questions chez cinq modèles d'algues vertes (Ostreococcus tauri, O. mediterraneus, Bathycoccus prasinos, Micromonas pusilla, et Picochlorum RCC4223). Il est mis en évidence une diminution de la fitness au cours du temps en raison des mutations délétères, et une importante interaction génotype-environnement sur l'effet des mutations. Le taux de mutation varie aux échelles intra-génomique et inter-spécifique, avec deux principaux résultats: une augmentation du taux de mutation dans les régions non codantes et une augmentation du taux de mutation avec la taille du génome chez les eucaryotes et en fonction de l'écart à l'équilibre en GC du génome. Aussi, l'assemblage et l'annotation d'une picoalgue du genre Picochlorum permettent d'étudier le rôle des transferts horizontaux de gènes chez les Chlorophytes

The Location of the Pseudoautosomal Boundary in Silene latifolia

Y-chromosomes contain a non-recombining region (NRY), and in many organisms it was shown that the NRY expanded over time. How and why the NRY expands remains unclear. Young sex chromosomes, where NRY expansion occurred recently or is on-going, offer an opportunity to study the causes of this process. Here, we used the plant Silene latifolia, where sex chromosomes evolved ~11 million years ago, to study the location of the boundary between the NRY and the recombining pseudoautosomal region (PAR). The previous work devoted to the NRY/PAR boundary in S. latifolia was based on a handful of genes with locations approximately known from the genetic map. Here, we report the analysis of 86 pseudoautosomal and sex-linked genes adjacent to the S. latifolia NRY/PAR boundary to establish the location of the boundary more precisely. We take advantage of the dense genetic map and polymorphism data from wild populations to identify 20 partially sex-linked genes located in the “fuzzy boundary”, that rarely recombines in male meiosis. Genes proximal to this fuzzy boundary show no evidence of recombination in males, while the genes distal to this partially-sex-linked region are actively recombining in males. Our results provide a more accurate location for the PAR boundary in S. latifolia, which will help to elucidate the causes of PAR boundary shifts leading to NRY expansion over time

Codon usage bias in phytoplankton

Non-random usage of synonymous codons, known as “codon bias”, has been described in many organisms, from bacteria to Drosophila, but little is known about it in phytoplankton. This phenomenon is thought to be driven by selection for translational efficiency. As the efficacy of selection is proportional to the effective population size, species with large population sizes, such as phytoplankton, are expected to have strong codon bias. To test this, we measured codon bias in 215 strains from Haptophyta, Chlorophyta, Ochrophyta (except diatoms that were studied previously), Dinophyta, Cryptophyta, Ciliophora, unicellular Rhodophyta and Chlorarachniophyta. Codon bias is modest in most groups, despite the astronomically large population sizes of marine phytoplankton. The strength of the codon bias, measured with the effective number of codons, is the strongest in Haptophyta and the weakest in Chlorarachniophyta. The optimal codons are GC-ending in most cases, but several shifts to AT-ending codons were observed (mainly in Ochrophyta and Ciliophora). As it takes a long time to reach a new equilibrium after such shifts, species having AT-ending codons show a lower frequency of optimal codons compared to other species. Genetic diversity, calculated for species with more than three strains sequenced, is modest, indicating that the effective population sizes are many orders of magnitude lower than the astronomically large census population sizes, which helps to explain the modest codon bias in marine phytoplankton. This study represents the first comparative analysis of codon bias across multiple major phytoplankton groups

Evolution of mutation rate in astronomically large phytoplankton populations

Genetic diversity is expected to be proportional to population size, yet, there is a well-known, but unexplained lack of genetic diversity in large populations – the “Lewontin’s paradox”. Larger populations are expected to evolve lower mutation rates, which may help to explain this paradox. Here we test this conjecture by measuring the spontaneous mutation rate in a ubiquitous unicellular marine phytoplankton species Emiliania huxleyi (Haptophyta) that has modest genetic diversity despite an astronomically large population size. Genome sequencing of E. huxleyi mutation accumulation lines revealed 455 mutations, with an unusual GC-biased mutation spectrum. This yielded an estimate of the per site mutation rate µ=5.55x10−10 (CI 95%: 5.05x10−10 – 6.09x10−10), which corresponds to an effective population size Ne∼2.7x106. Such a modest Ne is surprising for a ubiquitous and abundant species that accounts for up to 10% of global primary productivity in the oceans. Our results indicate that even exceptionally large populations do not evolve mutation rates lower than ∼10−10 per nucleotide per cell division. They rule out the possibility that the extreme disparity between modest genetic diversity and astronomically large population size in the plankton species is due to an unusually low mutation rate

First estimation of the spontaneous mutation rate in Diatoms

International audienceMutations are the origin of genetic diversity, and the mutation rate is a fundamental parameter to understand all aspects of molecular evolution. The combination of mutation-accumulation experiments and high throughput sequencing enabled the estimation of mutation rates in most model organisms, but several major eukaryotic lineages remain unexplored. Here, we report the first estimation of the spontaneous mutation rate in a model unicellular eukaryote from the Stramenopile kingdom, the diatom Phaeodactylum tricornutum (strain RCC2967). We sequenced 36 mutation accumulation lines for an average of 181 generations per line and identified 156 de novo mutations. The base substitution mutation rate per site per generation is μbs = 4.77x10-10 and the insertion-deletion mutation rate is μid = 1.58x10-11. The mutation rate varies as a function of the nucleotide context and is biased towards an excess of mutations from GC to AT, consistent with previous observations in other species. Interestingly, the mutation rates between the genomes of organelles and the nucleus differ, with a significantly higher mutation rate in the mitochondria. This confirms previous claims based on indirect estimations of the mutation rate in mitochondria of photosynthetic eukaryotes that acquired their plastid through a secondary endosymbiosis. This novel estimate enables us to infer the effective population size of P. tricornutum to be Ne~8.72x10 6